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When and how data is presented to a user is based on their user roles, which are specified in the PM Cell. Each user will have at least two roles per user_id and product_id combination. These two roles can be further defined as a Data Protection role and a Hive Management role.
The data protection role establishes the detail of data the user can see while the hive managment role defines their level of functionality the user has in a project.The following tables summarize the roles in a hierarchical order of least to most access.

Data Protection Track

 

Role

Access Description

DATA_OBFSC

OBFSC = Obfuscated

  • The user can see aggregated results that are obfuscated (example: patient count).
  • The user is limited on the number of times they can run the same query within a specified time period. If the user exceeds the maximum number of times then their account will be locked and only the Admin user can unlock it.

DATA_AGG

AGG = Aggregated

  • The user can see aggregated results like the patient count.
  • The results are not obfuscated and the user is not limited to the number of times they can run the same query.

DATA_LDS

LDS = Limited Data Set

  • The user can see all fields except for those that are encrypted.
  • An example of an encrypted field is the blob fields in the fact and dimension tables.

DATA_DEID

DEID = De-identified Data

  • The user can see all fields including those that are encrypted.
  • An example of an encrypted field is the blob fields in the fact and dimension tables.

DATA_PROT

PROT = Protected

  • The user can see all data, including the identified data that resides in the Identity Management Cell.

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The ONT service is designed as a collection of operations or use cases:

Service Operation

Description

getCategories

Returns a list of categories available for a given user. These categories are displayed in a tree format. The top level of the tree consists of all the categories a particular user has permission to see.

getChildren

Expands any level of a vocabulary category, providing information about its children, for a given user.

getSchemes

Returns a list of schemes available in the system. This operation basically provides information about the different kinds of coding systems that exist.

getNameInfo

Returns information needed about all nodes related to a given search keyword or name.

getCodeInfo

Returns information about a code, such as the name associated with a particular code.

getTermInfo

Returns information about a particular node.

addChild

Adds a new Ontology term to the tree under the selected parent node.

deleteChild

Deletes a selected Ontology term.

modifyChild

Modifies content within an existing Ontology term

updateCRCConcept

Notifies the Ontology cell to synchronize metadata terms with concept_dimension table

getProcessStatus

Returns status information about the concept_dimension synchronization process

getDirtyState

Returns state information about the need to synchronize with the concept_dimension table

updateConceptTotalNum

Notifies the Ontology cell to get patient count from CRC for this concept and then update the totalnum for this concept in the metadata table.

getModifiers

Returns list of modifiers for a concept if they exist.

getModifierChildren

Expands any level of a modifier folder, providing information about its children.

getModifierInfo

Returns information about a particular modifier.

getModifierNameInfo

Returns modifiers associated with a concept that meet a name search criteria

getModifierCodeInfo

Returns modifiers associated with a concept that meet a code search criteria.

addModifier

Adds a new Ontology modifier to the tree under the selected parent node or modifier.

excludeModifier

Excludes an existing modifier from a concept lower in the hierarchy than the modifier's specified hierarchy level.

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This section provides a description of the architecture as multiple views. Each view conveys the different attributes of the architecture.

  1. Components and Connector View
  2. Client-Server Style

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Metadatai2b2
WorkbenchOntology
Management
ServerProject
Management
ServerREST/SOAPREST/SOAPJDBC*Server*Client

Anchor
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_Toc161583412
3.1.1.2 Element Catalog

Element Name

Type

Description

i2b2 Workbench

Client Component

Webservice client submits the requests to ONT Server components and renders response XML.

Ontology Management Server

Server Component

Provides Web Service Interface for the ONT system.
It supports the REST or SOAP protocol.
It directs the user to the correct data source associated with the project.
It uses Project Management server to handle user authentication.

Project Management Server

Server Component

ONT cell uses Project Management cell to authenticate user.
ONT cell constructs PM request message and makes a web service call to Project Management Cell.

Metadata

Data Repository Component

This repository is a database for i2b2 metadata.

JDBC

Query Connector

SQL query used as a connector between the ONT System and the Metadata database.

Web Service

Request Connector

REST protocol used to communicate with the external system.

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